PXD054023-1

PXD054023 is an original dataset announced via ProteomeXchange.

Title	Exploring the TDP-43 interactome in the nucleus and cytoplasm
Description	Cytoplasmic aggregation TAR DNA binding protein 43 (TDP-43) is a hallmark pathology of motor neuron disease (MND), amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD) and limbic-predominant age-related TDP-43 encephalopathy (LATE). The disease-relevant protein-protein interactome of TDP-43 remains incompletely defined, elucidation of which will increase understanding of the molecular mechanisms responsible for disease. In this study, we aimed to identify true TDP-43 protein partners within the nucleus and cytoplasm and interactions at specific pathological stages of disease by correlating identified TDP-43 interaction partners in in human embryonic kidney HEK293, mouse neuroblastoma Neuro2A and mouse primary neurons. Using this approach combined with APEX2 proximity labelling and immunoprecipitation, and coupled with mass spectrometry analysis of protein interactors from nuclear and cytoplasmic fractions, we identified 58 putative wild-type TDP-43 interactors, including novel binding partners responsible for RNA metabolism and splicing. We verified the level of interaction of these protein partners in two other models: (1) a model presenting early pathological change showing TDP-43WT condensates in the nucleus through arsenite treatment and (2) a model stimulating another early-disease stage with TDP-43 containing ALS missense mutations (G294V and A315T) in the nucleus. We found that most interactors that presenting had a weaker affinity to mutant TDP-43 in the cytoplasm are involved in the translational machinery which could, over time, contribute to neurodegeneration. Understanding early pathological changes to TDP-43 in the nucleus and its specific interactions partners at different disease stages is critical to better understand ALS and FTLD mechanisms and provide potential therapeutic targets and novel biomarkers.
HostingRepository	PRIDE
AnnounceDate	2025-05-14
AnnouncementXML	Submission_2025-05-14_05:44:33.668.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD054023
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Albert Lee
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	biotinylated residue; acetylated residue; monohydroxylated residue; deaminated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-17 17:03:52	ID requested
⏵ 1	2025-05-14 05:44:34	announced

10.6019/PXD054023;

10.1111/JNC.70079;

submitter keyword: APEX,IP, TDP-43, LC-MS/MS

Albert Lee
contact affiliation	Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health, and Human Sciences, Macquarie University, North Ryde, NSW, Australia.
contact email	albert.lee@mq.edu.au
lab head
Albert Lee
contact affiliation	Macquarie University
contact email	albert.lee@mq.edu.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD054023
     1. Label: PRIDE project
     2. Name: Exploring the TDP-43 interactome in the nucleus and cytoplasm